rs6498015

Variant names:

• chr16-27380303-A-G
• rs6498015

Your query was ambiguous. Multiple possible variants found:

• chr16-27380303-A-G
• chr16-27380303-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.891 in 152,274 control chromosomes in the GnomAD database, including 60,770 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.89 (60770 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.891 AC: 135619 AN: 152156 Hom.: 60713 Cov.: 33

Gnomad AFR AF: 0.963

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.880

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.891 AC: 135733 AN: 152274 Hom.: 60770 Cov.: 33 AF XY: 0.890 AC XY: 66259 AN XY: 74440

African (AFR) AF: 0.963 AC: 40039 AN: 41562

American (AMR) AF: 0.865 AC: 13234 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.906 AC: 3145 AN: 3472

East Asian (EAS) AF: 0.681 AC: 3528 AN: 5178

South Asian (SAS) AF: 0.897 AC: 4331 AN: 4830

European-Finnish (FIN) AF: 0.861 AC: 9114 AN: 10588

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59465 AN: 68030

Other (OTH) AF: 0.880 AC: 1856 AN: 2110

Alfa AF: 0.884 Hom.: 17445

Bravo AF: 0.891

Asia WGS AF: 0.808 AC: 2810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.092
DANN	Benign	0.23
PhyloP100		-1.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6498015; hg19: chr16-27391624;